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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggaatccctcgccatgtttacgccttcggtttacttcctttgatctgactaggtttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG

Basic information

species Zea mays
transcript GRMZM2G101412_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101412_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g52410.1 (Oryza sativa), 3'ss of exon 1
gtgagtggaatccc---tcgccatgtttacgccttcggttt--acttcctttgatctgactagg---------------tttgtttc-agGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG
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gtgagctgaatctcgcgtcgccatctctgcaccttggtccttgggtttattcgatctgattcgtgcgctgtatcgaactcttgtttctagGTGAGGAAGTGGTGGAGTATACGGAGGAGCAGATTAGGAAGGCGGAGGAGTCGATCCGGATTCGCCGCGAGGCGGAGCCCGTCGAGCTTGTCGAGGCG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78106195|gb|DV524613.1|DV524613
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|91050680|gb|EB161098.1|EB161098
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|93281054|gb|EB673318.1|EB673318
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|149008563|gb|EE040740.2|EE040740
EST:     GCTCCGCTCCCTCCCCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAAAC                         GCGGGGAAGTGGGGCCGTACACG
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACG
EST: gi|76015302|gb|DT942472.1|DT942472
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|110193828|gb|EC875726.1|EC875726
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|89253067|gb|DY624853.1|DY624853
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|78091707|gb|DV520081.1|DV520081
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
EST: gi|76922300|gb|DV168931.1|DV168931
EST:     GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACC                         GCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT
genomic: GCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 41 (upstream exon), 49 (downstream exon)
Score: 59

CGCGTCACCGTGGCCGTCTGCATCGGCAACCTTGTCGCCGTGCTGCTCGTGCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 99

CGCGTCACCGTGGCCGTCTGCATCGGCAACCTTGTCGCCGTGCTGCTCGTGCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

CGCGTCACCGTGGCCGTCTGCATCGGCAACCTTGTCGCCGTGCTGCTCGTGCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

CGCGTCACCGTGGCCGTCTGCATCGGCAACCTTGTCGCCGTGCTGCTCGTGCTCCGCTCCCTCACCGCCCCCGCTTCCTTCGCACCCACCGCTCCCAACCgtgagtggaa ... tttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgccatgtttacgccttcggtttacttcctttgatctgactaggtttgtttcagGCGGGGAAGTGGTGCAGTACACGGAGGAGCAGATTAGGTGGGTGGAGGAGTCGATCCGGATTCGCCGCGAGGCTGAGCCCGTCGAGCTCGTTCTGGCG
                                  atctgac  putative branch site (score: 146)
                                             tttgtttc  putative PPT
     atgttta  TA-rich tract